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revision 1.15, Wed Jun 22 21:30:45 2005 UTC revision 1.47, Thu Oct 20 12:02:43 2005 UTC
# Line 70  Line 70 
70    
71  * B<maxSequenceLength> maximum number of residues per sequence, (default C<8000>)  * B<maxSequenceLength> maximum number of residues per sequence, (default C<8000>)
72    
73    * B<noDBOpen> suppresses the connection to the database if TRUE, else FALSE
74    
75  =back  =back
76    
77  For example, the following constructor call specifies a database named I<Sprout> and a user name of  For example, the following constructor call specifies a database named I<Sprout> and a user name of
# Line 86  Line 88 
88      # Compute the options. We do this by starting with a table of defaults and overwriting with      # Compute the options. We do this by starting with a table of defaults and overwriting with
89      # the incoming data.      # the incoming data.
90      my $optionTable = Tracer::GetOptions({      my $optionTable = Tracer::GetOptions({
91                         dbType       => 'mysql',         # database type                         dbType       => $FIG_Config::dbms,
92                         dataDir      => 'Data',          # data file directory                                                          # database type
93                         xmlFileName  => 'SproutDBD.xml', # database definition file name                         dataDir      => $FIG_Config::sproutData,
94                         userData     => 'root/',         # user name and password                                                          # data file directory
95                         port         => 0,               # database connection port                         xmlFileName  => "$FIG_Config::sproutData/SproutDBD.xml",
96                                                            # database definition file name
97                           userData     => "$FIG_Config::dbuser/$FIG_Config::dbpass",
98                                                            # user name and password
99                           port         => $FIG_Config::dbport,
100                                                            # database connection port
101                         maxSegmentLength => 4500,        # maximum feature segment length                         maxSegmentLength => 4500,        # maximum feature segment length
102                         maxSequenceLength => 8000,       # maximum contig sequence length                         maxSequenceLength => 8000,       # maximum contig sequence length
103                           noDBOpen     => 0,               # 1 to suppress the database open
104                        }, $options);                        }, $options);
105      # Get the data directory.      # Get the data directory.
106      my $dataDir = $optionTable->{dataDir};      my $dataDir = $optionTable->{dataDir};
# Line 100  Line 108 
108      $optionTable->{userData} =~ m!([^/]*)/(.*)$!;      $optionTable->{userData} =~ m!([^/]*)/(.*)$!;
109      my ($userName, $password) = ($1, $2);      my ($userName, $password) = ($1, $2);
110      # Connect to the database.      # Connect to the database.
111      my $dbh = DBKernel->new($optionTable->{dbType}, $dbName, $userName, $password, $optionTable->{port});      my $dbh;
112        if (! $optionTable->{noDBOpen}) {
113            $dbh = DBKernel->new($optionTable->{dbType}, $dbName, $userName,
114                                    $password, $optionTable->{port});
115        }
116      # Create the ERDB object.      # Create the ERDB object.
117      my $xmlFileName = "$optionTable->{xmlFileName}";      my $xmlFileName = "$optionTable->{xmlFileName}";
118      my $erdb = ERDB->new($dbh, $xmlFileName);      my $erdb = ERDB->new($dbh, $xmlFileName);
# Line 377  Line 389 
389    
390  =head3 LoadUpdate  =head3 LoadUpdate
391    
392  C<< my %stats = $sprout->LoadUpdate($truncateFlag, \@tableList); >>  C<< my $stats = $sprout->LoadUpdate($truncateFlag, \@tableList); >>
393    
394  Load updates to one or more database tables. This method enables the client to make changes to one  Load updates to one or more database tables. This method enables the client to make changes to one
395  or two tables without reloading the whole database. For each table, there must be a corresponding  or two tables without reloading the whole database. For each table, there must be a corresponding
# Line 420  Line 432 
432      # Loop through the incoming table names.      # Loop through the incoming table names.
433      for my $tableName (@{$tableList}) {      for my $tableName (@{$tableList}) {
434          # Find the table's file.          # Find the table's file.
435          my $fileName = "$dataDir/$tableName";          my $fileName = LoadFileName($dataDir, $tableName);
436          if (! -e $fileName) {          if (! $fileName) {
437              $fileName = "$fileName.dtx";              Trace("No load file found for $tableName in $dataDir.") if T(0);
438          }          } else {
439          # Attempt to load this table.          # Attempt to load this table.
440          my $result = $erdb->LoadTable($fileName, $tableName, $truncateFlag);          my $result = $erdb->LoadTable($fileName, $tableName, $truncateFlag);
441          # Accumulate the resulting statistics.          # Accumulate the resulting statistics.
442          $retVal->Accumulate($result);          $retVal->Accumulate($result);
443      }      }
444        }
445      # Return the statistics.      # Return the statistics.
446      return $retVal;      return $retVal;
447  }  }
# Line 570  Line 583 
583  =item RETURN  =item RETURN
584    
585  Returns a list of the feature's contig segments. The locations are returned as a list in a list  Returns a list of the feature's contig segments. The locations are returned as a list in a list
586  context and as a space-delimited string in a scalar context.  context and as a comma-delimited string in a scalar context.
587    
588  =back  =back
589    
# Line 597  Line 610 
610          if ($prevContig eq $contigID && $dir eq $prevDir) {          if ($prevContig eq $contigID && $dir eq $prevDir) {
611              # Here the new segment is in the same direction on the same contig. Insure the              # Here the new segment is in the same direction on the same contig. Insure the
612              # new segment's beginning is next to the old segment's end.              # new segment's beginning is next to the old segment's end.
613              if (($dir eq "-" && $beg == $prevBeg - $prevLen) ||              if ($dir eq "-" && $beg + $len == $prevBeg) {
614                  ($dir eq "+" && $beg == $prevBeg + $prevLen)) {                  # Here we're merging two backward blocks, so we keep the new begin point
615                  # Here we need to merge two segments. Adjust the beginning and length values                  # and adjust the length.
616                  # to include both segments.                  $len += $prevLen;
617                    # Pop the old segment off. The new one will replace it later.
618                    pop @retVal;
619                } elsif ($dir eq "+" && $beg == $prevBeg + $prevLen) {
620                    # Here we need to merge two forward blocks. Adjust the beginning and
621                    # length values to include both segments.
622                  $beg = $prevBeg;                  $beg = $prevBeg;
623                  $len += $prevLen;                  $len += $prevLen;
624                  # Pop the old segment off. The new one will replace it later.                  # Pop the old segment off. The new one will replace it later.
# Line 609  Line 627 
627          }          }
628          # Remember this specifier for the adjacent-segment test the next time through.          # Remember this specifier for the adjacent-segment test the next time through.
629          ($prevContig, $prevBeg, $prevDir, $prevLen) = ($contigID, $beg, $dir, $len);          ($prevContig, $prevBeg, $prevDir, $prevLen) = ($contigID, $beg, $dir, $len);
630            # Compute the initial base pair.
631            my $start = ($dir eq "+" ? $beg : $beg + $len - 1);
632          # Add the specifier to the list.          # Add the specifier to the list.
633          push @retVal, "${contigID}_$beg$dir$len";          push @retVal, "${contigID}_$start$dir$len";
634      }      }
635      # Return the list in the format indicated by the context.      # Return the list in the format indicated by the context.
636      return (wantarray ? @retVal : join(' ', @retVal));      return (wantarray ? @retVal : join(',', @retVal));
637  }  }
638    
639  =head3 ParseLocation  =head3 ParseLocation
# Line 644  Line 664 
664      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
665      my ($location) = @_;      my ($location) = @_;
666      # Parse it into segments.      # Parse it into segments.
667      $location =~ /^(.*)_(\d*)([+-_])(\d*)$/;      $location =~ /^(.+)_(\d+)([+\-_])(\d+)$/;
668      my ($contigID, $start, $dir, $len) = ($1, $2, $3, $4);      my ($contigID, $start, $dir, $len) = ($1, $2, $3, $4);
669      # If the direction is an underscore, convert it to a + or -.      # If the direction is an underscore, convert it to a + or -.
670      if ($dir eq "_") {      if ($dir eq "_") {
# Line 752  Line 772 
772          # the start point is the ending. Note that in the latter case we must reverse the DNA string          # the start point is the ending. Note that in the latter case we must reverse the DNA string
773          # before putting it in the return value.          # before putting it in the return value.
774          my ($start, $stop);          my ($start, $stop);
775            Trace("Parse of \"$location\" is $beg$dir$len.") if T(SDNA => 4);
776          if ($dir eq "+") {          if ($dir eq "+") {
777              $start = $beg;              $start = $beg;
778              $stop = $beg + $len - 1;              $stop = $beg + $len - 1;
779          } else {          } else {
780              $start = $beg + $len + 1;              $start = $beg - $len + 1;
781              $stop = $beg;              $stop = $beg;
782          }          }
783            Trace("Looking for sequences containing $start through $stop.") if T(SDNA => 4);
784          my $query = $self->Get(['IsMadeUpOf','Sequence'],          my $query = $self->Get(['IsMadeUpOf','Sequence'],
785              "IsMadeUpOf(from-link) = ? AND IsMadeUpOf(start-position) + IsMadeUpOf(len) > ? AND " .              "IsMadeUpOf(from-link) = ? AND IsMadeUpOf(start-position) + IsMadeUpOf(len) > ? AND " .
786              " IsMadeUpOf(start-position) <= ? ORDER BY IsMadeUpOf(start-position)",              " IsMadeUpOf(start-position) <= ? ORDER BY IsMadeUpOf(start-position)",
# Line 770  Line 792 
792                  $sequence->Values(['IsMadeUpOf(start-position)', 'Sequence(sequence)',                  $sequence->Values(['IsMadeUpOf(start-position)', 'Sequence(sequence)',
793                                     'IsMadeUpOf(len)']);                                     'IsMadeUpOf(len)']);
794              my $stopPosition = $startPosition + $sequenceLength;              my $stopPosition = $startPosition + $sequenceLength;
795                Trace("Sequence is from $startPosition to $stopPosition.") if T(SDNA => 4);
796              # Figure out the start point and length of the relevant section.              # Figure out the start point and length of the relevant section.
797              my $pos1 = ($start < $startPosition ? 0 : $start - $startPosition);              my $pos1 = ($start < $startPosition ? 0 : $start - $startPosition);
798              my $len = ($stopPosition <= $stop ? $stopPosition : $stop) - $startPosition - $pos1;              my $len1 = ($stopPosition < $stop ? $stopPosition : $stop) + 1 - $startPosition - $pos1;
799                Trace("Position is $pos1 for length $len1.") if T(SDNA => 4);
800              # Add the relevant data to the location data.              # Add the relevant data to the location data.
801              $locationDNA .= substr($sequenceData, $pos1, $len);              $locationDNA .= substr($sequenceData, $pos1, $len1);
802          }          }
803          # Add this location's data to the return string. Note that we may need to reverse it.          # Add this location's data to the return string. Note that we may need to reverse it.
804          if ($dir eq '+') {          if ($dir eq '+') {
805              $retVal .= $locationDNA;              $retVal .= $locationDNA;
806          } else {          } else {
807              $locationDNA = join('', reverse split //, $locationDNA);              $retVal .= FIG::reverse_comp($locationDNA);
             $retVal .= $locationDNA;  
808          }          }
809      }      }
810      # Return the result.      # Return the result.
# Line 851  Line 874 
874      # Set it from the sequence data, if any.      # Set it from the sequence data, if any.
875      if ($sequence) {      if ($sequence) {
876          my ($start, $len) = $sequence->Values(['IsMadeUpOf(start-position)', 'IsMadeUpOf(len)']);          my ($start, $len) = $sequence->Values(['IsMadeUpOf(start-position)', 'IsMadeUpOf(len)']);
877          $retVal = $start + $len;          $retVal = $start + $len - 1;
878        }
879        # Return the result.
880        return $retVal;
881    }
882    
883    =head3 ClusterPEGs
884    
885    C<< my $clusteredList = $sprout->ClusterPEGs($sub, \@pegs); >>
886    
887    Cluster the PEGs in a list according to the cluster coding scheme of the specified
888    subsystem. In order for this to work properly, the subsystem object must have
889    been used recently to retrieve the PEGs using the B<get_pegs_from_cell> method.
890    This causes the cluster numbers to be pulled into the subsystem's color hash.
891    If a PEG is not found in the color hash, it will not appear in the output
892    sequence.
893    
894    =over 4
895    
896    =item sub
897    
898    Sprout subsystem object for the relevant subsystem, from the L</get_subsystem>
899    method.
900    
901    =item pegs
902    
903    Reference to the list of PEGs to be clustered.
904    
905    =item RETURN
906    
907    Returns a list of the PEGs, grouped into smaller lists by cluster number.
908    
909    =back
910    
911    =cut
912    #: Return Type $@@;
913    sub ClusterPEGs {
914        # Get the parameters.
915        my ($self, $sub, $pegs) = @_;
916        # Declare the return variable.
917        my $retVal = [];
918        # Loop through the PEGs, creating arrays for each cluster.
919        for my $pegID (@{$pegs}) {
920            my $clusterNumber = $sub->get_cluster_number($pegID);
921            # Only proceed if the PEG is in a cluster.
922            if ($clusterNumber >= 0) {
923                # Push this PEG onto the sub-list for the specified cluster number.
924                push @{$retVal->[$clusterNumber]}, $pegID;
925            }
926      }      }
927      # Return the result.      # Return the result.
928      return $retVal;      return $retVal;
# Line 1001  Line 1072 
1072    
1073  =head3 FeatureAnnotations  =head3 FeatureAnnotations
1074    
1075  C<< my @descriptors = $sprout->FeatureAnnotations($featureID); >>  C<< my @descriptors = $sprout->FeatureAnnotations($featureID, $rawFlag); >>
1076    
1077  Return the annotations of a feature.  Return the annotations of a feature.
1078    
# Line 1011  Line 1082 
1082    
1083  ID of the feature whose annotations are desired.  ID of the feature whose annotations are desired.
1084    
1085    =item rawFlag
1086    
1087    If TRUE, the annotation timestamps will be returned in raw form; otherwise, they
1088    will be returned in human-readable form.
1089    
1090  =item RETURN  =item RETURN
1091    
1092  Returns a list of annotation descriptors. Each descriptor is a hash with the following fields.  Returns a list of annotation descriptors. Each descriptor is a hash with the following fields.
1093    
1094  * B<featureID> ID of the relevant feature.  * B<featureID> ID of the relevant feature.
1095    
1096  * B<timeStamp> time the annotation was made, in user-friendly format.  * B<timeStamp> time the annotation was made.
1097    
1098  * B<user> ID of the user who made the annotation  * B<user> ID of the user who made the annotation
1099    
# Line 1029  Line 1105 
1105  #: Return Type @%;  #: Return Type @%;
1106  sub FeatureAnnotations {  sub FeatureAnnotations {
1107      # Get the parameters.      # Get the parameters.
1108      my ($self, $featureID) = @_;      my ($self, $featureID, $rawFlag) = @_;
1109      # Create a query to get the feature's annotations and the associated users.      # Create a query to get the feature's annotations and the associated users.
1110      my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],      my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],
1111                             "IsTargetOfAnnotation(from-link) = ?", [$featureID]);                             "IsTargetOfAnnotation(from-link) = ?", [$featureID]);
# Line 1042  Line 1118 
1118              $annotation->Values(['IsTargetOfAnnotation(from-link)',              $annotation->Values(['IsTargetOfAnnotation(from-link)',
1119                                   'Annotation(time)', 'MadeAnnotation(from-link)',                                   'Annotation(time)', 'MadeAnnotation(from-link)',
1120                                   'Annotation(annotation)']);                                   'Annotation(annotation)']);
1121            # Convert the time, if necessary.
1122            if (! $rawFlag) {
1123                $timeStamp = FriendlyTimestamp($timeStamp);
1124            }
1125          # Assemble them into a hash.          # Assemble them into a hash.
1126          my $annotationHash = { featureID => $featureID,          my $annotationHash = { featureID => $featureID,
1127                                 timeStamp => FriendlyTimestamp($timeStamp),                                 timeStamp => $timeStamp,
1128                                 user => $user, text => $text };                                 user => $user, text => $text };
1129          # Add it to the return list.          # Add it to the return list.
1130          push @retVal, $annotationHash;          push @retVal, $annotationHash;
# Line 1073  Line 1153 
1153    
1154  =item RETURN  =item RETURN
1155    
1156  Returns a hash mapping the functional assignment IDs to user IDs.  Returns a hash mapping the user IDs to functional assignment IDs.
1157    
1158  =back  =back
1159    
# Line 1083  Line 1163 
1163      # Get the parameters.      # Get the parameters.
1164      my ($self, $featureID) = @_;      my ($self, $featureID) = @_;
1165      # Get all of the feature's annotations.      # Get all of the feature's annotations.
1166      my @query = $self->GetAll(['IsTargetOfAnnotation', 'Annotation'],      my @query = $self->GetAll(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],
1167                              "IsTargetOfAnnotation(from-link) = ?",                              "IsTargetOfAnnotation(from-link) = ?",
1168                              [$featureID], ['Annotation(time)', 'Annotation(annotation)']);                              [$featureID], ['Annotation(time)', 'Annotation(annotation)',
1169                                               'MadeAnnotation(from-link)']);
1170      # Declare the return hash.      # Declare the return hash.
1171      my %retVal;      my %retVal;
     # Declare a hash for insuring we only make one assignment per user.  
     my %timeHash = ();  
1172      # Now we sort the assignments by timestamp in reverse.      # Now we sort the assignments by timestamp in reverse.
1173      my @sortedQuery = sort { -($a->[0] <=> $b->[0]) } @query;      my @sortedQuery = sort { -($a->[0] <=> $b->[0]) } @query;
1174      # Loop until we run out of annotations.      # Loop until we run out of annotations.
1175      for my $annotation (@sortedQuery) {      for my $annotation (@sortedQuery) {
1176          # Get the annotation fields.          # Get the annotation fields.
1177          my ($timeStamp, $text) = @{$annotation};          my ($timeStamp, $text, $user) = @{$annotation};
1178          # Check to see if this is a functional assignment.          # Check to see if this is a functional assignment.
1179          my ($user, $function) = _ParseAssignment($text);          my ($type, $function) = _ParseAssignment($text);
1180          if ($user && ! exists $timeHash{$user}) {          if ($type && ! exists $retVal{$user}) {
1181              # Here it is a functional assignment and there has been no              # Here it is a functional assignment and there has been no
1182              # previous assignment for this user, so we stuff it in the              # previous assignment for this user, so we stuff it in the
1183              # return hash.              # return hash.
1184              $retVal{$function} = $user;              $retVal{$user} = $function;
             # Insure we don't assign to this user again.  
             $timeHash{$user} = 1;  
1185          }          }
1186      }      }
1187      # Return the hash of assignments found.      # Return the hash of assignments found.
# Line 1120  Line 1197 
1197  The functional assignment is handled differently depending on the type of feature. If  The functional assignment is handled differently depending on the type of feature. If
1198  the feature is identified by a FIG ID (begins with the string C<fig|>), then a functional  the feature is identified by a FIG ID (begins with the string C<fig|>), then a functional
1199  assignment is a type of annotation. The format of an assignment is described in  assignment is a type of annotation. The format of an assignment is described in
1200  L</ParseLocation>. Its worth noting that we cannot filter on the content of the  L</ParseAssignment>. Its worth noting that we cannot filter on the content of the
1201  annotation itself because it's a text field; however, this is not a big problem because  annotation itself because it's a text field; however, this is not a big problem because
1202  most features only have a small number of annotations.  most features only have a small number of annotations.
1203    
# Line 1211  Line 1288 
1288      return $retVal;      return $retVal;
1289  }  }
1290    
1291    =head3 FunctionsOf
1292    
1293    C<< my @functionList = $sprout->FunctionOf($featureID, $userID); >>
1294    
1295    Return the functional assignments of a particular feature.
1296    
1297    The functional assignment is handled differently depending on the type of feature. If
1298    the feature is identified by a FIG ID (begins with the string C<fig|>), then a functional
1299    assignment is a type of annotation. The format of an assignment is described in
1300    L</ParseAssignment>. Its worth noting that we cannot filter on the content of the
1301    annotation itself because it's a text field; however, this is not a big problem because
1302    most features only have a small number of annotations.
1303    
1304    If the feature is B<not> identified by a FIG ID, then the functional assignment
1305    information is taken from the B<ExternalAliasFunc> table. If the table does
1306    not contain an entry for the feature, an empty list is returned.
1307    
1308    =over 4
1309    
1310    =item featureID
1311    
1312    ID of the feature whose functional assignments are desired.
1313    
1314    =item RETURN
1315    
1316    Returns a list of 2-tuples, each consisting of a user ID and the text of an assignment by
1317    that user.
1318    
1319    =back
1320    
1321    =cut
1322    #: Return Type @@;
1323    sub FunctionsOf {
1324        # Get the parameters.
1325        my ($self, $featureID) = @_;
1326        # Declare the return value.
1327        my @retVal = ();
1328        # Determine the ID type.
1329        if ($featureID =~ m/^fig\|/) {
1330            # Here we have a FIG feature ID. We must build the list of trusted
1331            # users.
1332            my %trusteeTable = ();
1333            # Build a query for all of the feature's annotations, sorted by date.
1334            my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation'],
1335                                   "IsTargetOfAnnotation(from-link) = ? ORDER BY Annotation(time) DESC",
1336                                   [$featureID]);
1337            my $timeSelected = 0;
1338            # Loop until we run out of annotations.
1339            while (my $annotation = $query->Fetch()) {
1340                # Get the annotation text.
1341                my ($text, $time) = $annotation->Values(['Annotation(annotation)','Annotation(time)']);
1342                # Check to see if this is a functional assignment for a trusted user.
1343                my ($user, $function) = _ParseAssignment($text);
1344                if ($user) {
1345                    # Here it is a functional assignment.
1346                    push @retVal, [$user, $function];
1347                }
1348            }
1349        } else {
1350            # Here we have a non-FIG feature ID. In this case the user ID does not
1351            # matter. We simply get the information from the External Alias Function
1352            # table.
1353            push @retVal, $self->GetEntityValues('ExternalAliasFunc', $featureID, ['ExternalAliasFunc(func)']);
1354        }
1355        # Return the assignments found.
1356        return @retVal;
1357    }
1358    
1359  =head3 BBHList  =head3 BBHList
1360    
1361  C<< my $bbhHash = $sprout->BBHList($genomeID, \@featureList); >>  C<< my $bbhHash = $sprout->BBHList($genomeID, \@featureList); >>
# Line 1248  Line 1393 
1393          my $query = $self->Get(['IsBidirectionalBestHitOf'],          my $query = $self->Get(['IsBidirectionalBestHitOf'],
1394                                 "IsBidirectionalBestHitOf(from-link) = ? AND IsBidirectionalBestHitOf(genome) = ?",                                 "IsBidirectionalBestHitOf(from-link) = ? AND IsBidirectionalBestHitOf(genome) = ?",
1395                                 [$featureID, $genomeID]);                                 [$featureID, $genomeID]);
1396          # Look for the best hit.          # Peel off the BBHs found.
1397          my $bbh = $query->Fetch;          my @found = ();
1398          if ($bbh) {          while (my $bbh = $query->Fetch) {
1399              my ($targetFeature) = $bbh->Value('IsBidirectionalBestHitOf(to-link)');              push @found, $bbh->Value('IsBidirectionalBestHitOf(to-link)');
             $retVal{$featureID} = $targetFeature;  
1400          }          }
1401            $retVal{$featureID} = \@found;
1402      }      }
1403      # Return the mapping.      # Return the mapping.
1404      return \%retVal;      return \%retVal;
# Line 1506  Line 1651 
1651      my ($self, $peg1, $peg2) = @_;      my ($self, $peg1, $peg2) = @_;
1652      # Declare the return variable.      # Declare the return variable.
1653      my @retVal = ();      my @retVal = ();
1654      # Our first task is to find out the nature of the coupling.      # Our first task is to find out the nature of the coupling: whether or not
1655        # it exists, its score, and whether the features are stored in the same
1656        # order as the ones coming in.
1657      my ($couplingID, $inverted, $score) = $self->GetCoupling($peg1, $peg2);      my ($couplingID, $inverted, $score) = $self->GetCoupling($peg1, $peg2);
1658      # Only proceed if a coupling exists.      # Only proceed if a coupling exists.
1659      if ($couplingID) {      if ($couplingID) {
1660          # Determine the ordering to place on the evidence items. If we're          # Determine the ordering to place on the evidence items. If we're
1661          # inverted, we want to see feature 2 before feature 1; otherwise,          # inverted, we want to see feature 2 before feature 1 (descending); otherwise,
1662          # we want the reverse.          # we want feature 1 before feature 2 (normal).
1663            Trace("Coupling evidence for ($peg1, $peg2) with inversion flag $inverted.") if T(Coupling => 4);
1664          my $ordering = ($inverted ? "DESC" : "");          my $ordering = ($inverted ? "DESC" : "");
1665          # Get the coupling evidence.          # Get the coupling evidence.
1666          my @evidenceList = $self->GetAll(['IsEvidencedBy', 'PCH', 'UsesAsEvidence'],          my @evidenceList = $self->GetAll(['IsEvidencedBy', 'PCH', 'UsesAsEvidence'],
1667                                            "IsEvidencedBy(from-link) = ? ORDER BY PCH(id), UsesAsEvidence(pos) $ordering",                                            "IsEvidencedBy(from-link) = ? ORDER BY PCH(id), UsesAsEvidence(pos) $ordering",
1668                                            [$couplingID],                                            [$couplingID],
1669                                            ['PCH(used)', 'UsesAsEvidence(pos)']);                                            ['PCH(used)', 'UsesAsEvidence(to-link)']);
1670          # Loop through the evidence items. Each piece of evidence is represented by two          # Loop through the evidence items. Each piece of evidence is represented by two
1671          # positions in the evidence list, one for each feature on the other side of the          # positions in the evidence list, one for each feature on the other side of the
1672          # evidence link. If at some point we want to generalize to couplings with          # evidence link. If at some point we want to generalize to couplings with
# Line 1526  Line 1674 
1674          while (@evidenceList > 0) {          while (@evidenceList > 0) {
1675              my $peg1Data = shift @evidenceList;              my $peg1Data = shift @evidenceList;
1676              my $peg2Data = shift @evidenceList;              my $peg2Data = shift @evidenceList;
1677                Trace("Peg 1 is " . $peg1Data->[1] . " and Peg 2 is " . $peg2Data->[1] . ".") if T(Coupling => 4);
1678              push @retVal, [$peg1Data->[1], $peg2Data->[1], $peg1Data->[0]];              push @retVal, [$peg1Data->[1], $peg2Data->[1], $peg1Data->[0]];
1679          }          }
1680            Trace("Last index in evidence result is is $#retVal.") if T(Coupling => 4);
1681      }      }
     # TODO: code  
1682      # Return the result.      # Return the result.
1683      return @retVal;      return @retVal;
1684  }  }
# Line 1575  Line 1724 
1724      # Find the coupling data.      # Find the coupling data.
1725      my @pegs = $self->GetAll(['Coupling', 'ParticipatesInCoupling'],      my @pegs = $self->GetAll(['Coupling', 'ParticipatesInCoupling'],
1726                                   "Coupling(id) = ? ORDER BY ParticipatesInCoupling(pos)",                                   "Coupling(id) = ? ORDER BY ParticipatesInCoupling(pos)",
1727                                   [$retVal], "ParticipatesInCoupling(from-link), Coupling(score)");                                   [$retVal], ["ParticipatesInCoupling(from-link)", "Coupling(score)"]);
1728      # Check to see if we found anything.      # Check to see if we found anything.
1729      if (!@pegs) {      if (!@pegs) {
1730            Trace("No coupling found.") if T(Coupling => 4);
1731          # No coupling, so undefine the return value.          # No coupling, so undefine the return value.
1732          $retVal = undef;          $retVal = undef;
1733      } else {      } else {
1734          # We have a coupling! Get the score and check for inversion.          # We have a coupling! Get the score and check for inversion.
1735          $score = $pegs[0]->[1];          $score = $pegs[0]->[1];
1736          $inverted = ($pegs[0]->[0] eq $peg1);          my $firstFound = $pegs[0]->[0];
1737            $inverted = ($firstFound ne $peg1);
1738            Trace("Coupling score is $score. First peg is $firstFound, peg 1 is $peg1.") if T(Coupling => 4);
1739      }      }
1740      # Return the result.      # Return the result.
1741      return ($retVal, $inverted, $score);      return ($retVal, $inverted, $score);
# Line 1688  Line 1840 
1840          if ($line =~ m/^>\s*(.+?)(\s|\n)/) {          if ($line =~ m/^>\s*(.+?)(\s|\n)/) {
1841              # Here we have a new header. Store the current sequence if we have one.              # Here we have a new header. Store the current sequence if we have one.
1842              if ($id) {              if ($id) {
1843                  $retVal{$id} = uc $sequence;                  $retVal{$id} = lc $sequence;
1844              }              }
1845              # Clear the sequence accumulator and save the new ID.              # Clear the sequence accumulator and save the new ID.
1846              ($id, $sequence) = ("$prefix$1", "");              ($id, $sequence) = ("$prefix$1", "");
1847          } else {          } else {
1848              # Here we have a data line, so we add it to the sequence accumulator.              # Here we have a data line, so we add it to the sequence accumulator.
1849              # First, we get the actual data out. Note that we normalize to upper              # First, we get the actual data out. Note that we normalize to lower
1850              # case.              # case.
1851              $line =~ /^\s*(.*?)(\s|\n)/;              $line =~ /^\s*(.*?)(\s|\n)/;
1852              $sequence .= $1;              $sequence .= $1;
# Line 1702  Line 1854 
1854      }      }
1855      # Flush out the last sequence (if any).      # Flush out the last sequence (if any).
1856      if ($sequence) {      if ($sequence) {
1857          $retVal{$id} = uc $sequence;          $retVal{$id} = lc $sequence;
1858      }      }
1859      # Close the file.      # Close the file.
1860      close FASTAFILE;      close FASTAFILE;
# Line 2028  Line 2180 
2180      # Get the parameters.      # Get the parameters.
2181      my ($self, $entityName, $entityID) = @_;      my ($self, $entityName, $entityID) = @_;
2182      # Check for the entity instance.      # Check for the entity instance.
2183        Trace("Checking existence of $entityName with ID=$entityID.") if T(4);
2184      my $testInstance = $self->GetEntity($entityName, $entityID);      my $testInstance = $self->GetEntity($entityName, $entityID);
2185      # Return an existence indicator.      # Return an existence indicator.
2186      my $retVal = ($testInstance ? 1 : 0);      my $retVal = ($testInstance ? 1 : 0);
# Line 2219  Line 2372 
2372      return @retVal;      return @retVal;
2373  }  }
2374    
2375    =head3 GetProperties
2376    
2377    C<< my @list = $sprout->GetProperties($fid, $key, $value, $url); >>
2378    
2379    Return a list of the properties with the specified characteristics.
2380    
2381    Properties are arbitrary key-value pairs associated with a feature. (At some point they
2382    will also be associated with genomes.) A property value is represented by a 4-tuple of
2383    the form B<($fid, $key, $value, $url)>. These exactly correspond to the parameter
2384    
2385    =over 4
2386    
2387    =item fid
2388    
2389    ID of the feature possessing the property.
2390    
2391    =item key
2392    
2393    Name or key of the property.
2394    
2395    =item value
2396    
2397    Value of the property.
2398    
2399    =item url
2400    
2401    URL of the document that indicated the property should have this particular value, or an
2402    empty string if no such document exists.
2403    
2404    =back
2405    
2406    The parameters act as a filter for the desired data. Any non-null parameter will
2407    automatically match all the tuples returned. So, specifying just the I<$fid> will
2408    return all the properties of the specified feature; similarly, specifying the I<$key>
2409    and I<$value> parameters will return all the features having the specified property
2410    value.
2411    
2412    A single property key can have many values, representing different ideas about the
2413    feature in question. For example, one paper may declare that a feature C<fig|83333.1.peg.10> is
2414    virulent, and another may declare that it is not virulent. A query about the virulence of
2415    C<fig|83333.1.peg.10> would be coded as
2416    
2417        my @list = $sprout->GetProperties('fig|83333.1.peg.10', 'virulence', '', '');
2418    
2419    Here the I<$value> and I<$url> fields are left blank, indicating that those fields are
2420    not to be filtered. The tuples returned would be
2421    
2422        ('fig|83333.1.peg.10', 'virulence', 'yes', 'http://www.somewhere.edu/first.paper.pdf')
2423        ('fig|83333.1.peg.10', 'virulence', 'no', 'http://www.somewhere.edu/second.paper.pdf')
2424    
2425    =cut
2426    #: Return Type @@;
2427    sub GetProperties {
2428        # Get the parameters.
2429        my ($self, @parms) = @_;
2430        # Declare the return variable.
2431        my @retVal = ();
2432        # Now we need to create a WHERE clause that will get us the data we want. First,
2433        # we create a list of the columns containing the data for each parameter.
2434        my @colNames = ('HasProperty(from-link)', 'Property(property-name)',
2435                        'Property(property-value)', 'HasProperty(evidence)');
2436        # Now we build the WHERE clause and the list of parameter values.
2437        my @where = ();
2438        my @values = ();
2439        for (my $i = 0; $i <= $#colNames; $i++) {
2440            my $parm = $parms[$i];
2441            if (defined $parm && ($parm ne '')) {
2442                push @where, "$colNames[$i] = ?";
2443                push @values, $parm;
2444            }
2445        }
2446        # Format the WHERE clause.
2447        my $filter = (@values > 0 ? (join " AND ", @where) : undef);
2448        # Ask for all the propertie values with the desired characteristics.
2449        my $query = $self->Get(['HasProperty', 'Property'], $filter, \@values);
2450        while (my $valueObject = $query->Fetch()) {
2451            my @tuple = $valueObject->Values(\@colNames);
2452            push @retVal, \@tuple;
2453        }
2454        # Return the result.
2455        return @retVal;
2456    }
2457    
2458  =head3 FeatureProperties  =head3 FeatureProperties
2459    
2460  C<< my @properties = $sprout->FeatureProperties($featureID); >>  C<< my @properties = $sprout->FeatureProperties($featureID); >>
# Line 2413  Line 2649 
2649  C<< my %subsystems = $sprout->SubsystemsOf($featureID); >>  C<< my %subsystems = $sprout->SubsystemsOf($featureID); >>
2650    
2651  Return a hash describing all the subsystems in which a feature participates. Each subsystem is mapped  Return a hash describing all the subsystems in which a feature participates. Each subsystem is mapped
2652  to the role the feature performs.  to the roles the feature performs.
2653    
2654  =over 4  =over 4
2655    
# Line 2423  Line 2659 
2659    
2660  =item RETURN  =item RETURN
2661    
2662  Returns a hash mapping all the feature's subsystems to the feature's role.  Returns a hash mapping all the feature's subsystems to a list of the feature's roles.
2663    
2664  =back  =back
2665    
2666  =cut  =cut
2667  #: Return Type %;  #: Return Type %@;
2668  sub SubsystemsOf {  sub SubsystemsOf {
2669      # Get the parameters.      # Get the parameters.
2670      my ($self, $featureID) = @_;      my ($self, $featureID) = @_;
2671      # Use the SSCell to connect features to subsystems.      # Get the subsystem list.
2672      my @subsystems = $self->GetAll(['ContainsFeature', 'HasSSCell', 'IsRoleOf'],      my @subsystems = $self->GetAll(['ContainsFeature', 'HasSSCell', 'IsRoleOf'],
2673                                      "ContainsFeature(to-link) = ?", [$featureID],                                      "ContainsFeature(to-link) = ?", [$featureID],
2674                                      ['HasSSCell(from-link)', 'IsRoleOf(from-link)']);                                      ['HasSSCell(from-link)', 'IsRoleOf(from-link)']);
2675      # Create the return value.      # Create the return value.
2676      my %retVal = ();      my %retVal = ();
2677        # Build a hash to weed out duplicates. Sometimes the same PEG and role appears
2678        # in two spreadsheet cells.
2679        my %dupHash = ();
2680      # Loop through the results, adding them to the hash.      # Loop through the results, adding them to the hash.
2681      for my $record (@subsystems) {      for my $record (@subsystems) {
2682          $retVal{$record->[0]} = $record->[1];          # Get this subsystem and role.
2683            my ($subsys, $role) = @{$record};
2684            # Insure it's the first time for both.
2685            my $dupKey = "$subsys\n$role";
2686            if (! exists $dupHash{"$subsys\n$role"}) {
2687                $dupHash{$dupKey} = 1;
2688                push @{$retVal{$subsys}}, $role;
2689            }
2690      }      }
2691      # Return the hash.      # Return the hash.
2692      return %retVal;      return %retVal;
2693  }  }
2694    
2695    =head3 SubsystemList
2696    
2697    C<< my @subsystems = $sprout->SubsystemList($featureID); >>
2698    
2699    Return a list containing the names of the subsystems in which the specified
2700    feature participates. Unlike L</SubsystemsOf>, this method only returns the
2701    subsystem names, not the roles.
2702    
2703    =over 4
2704    
2705    =item featureID
2706    
2707    ID of the feature whose subsystem names are desired.
2708    
2709    =item RETURN
2710    
2711    Returns a list of the names of the subsystems in which the feature participates.
2712    
2713    =back
2714    
2715    =cut
2716    #: Return Type @;
2717    sub SubsystemList {
2718        # Get the parameters.
2719        my ($self, $featureID) = @_;
2720        # Get the list of names.
2721        my @retVal = $self->GetFlat(['ContainsFeature', 'HasSSCell'], "ContainsFeature(to-link) = ?",
2722                                    [$featureID], 'HasSSCell(from-link)');
2723        # Return the result.
2724        return @retVal;
2725    }
2726    
2727  =head3 RelatedFeatures  =head3 RelatedFeatures
2728    
2729  C<< my @relatedList = $sprout->RelatedFeatures($featureID, $function, $userID); >>  C<< my @relatedList = $sprout->RelatedFeatures($featureID, $function, $userID); >>
# Line 2864  Line 3142 
3142      return %retVal;      return %retVal;
3143  }  }
3144    
3145    =head3 MyGenomes
3146    
3147    C<< my @genomes = Sprout::MyGenomes($dataDir); >>
3148    
3149    Return a list of the genomes to be included in the Sprout.
3150    
3151    This method is provided for use during the Sprout load. It presumes the Genome load file has
3152    already been created. (It will be in the Sprout data directory and called either C<Genome>
3153    or C<Genome.dtx>.) Essentially, it reads in the Genome load file and strips out the genome
3154    IDs.
3155    
3156    =over 4
3157    
3158    =item dataDir
3159    
3160    Directory containing the Sprout load files.
3161    
3162    =back
3163    
3164    =cut
3165    #: Return Type @;
3166    sub MyGenomes {
3167        # Get the parameters.
3168        my ($dataDir) = @_;
3169        # Compute the genome file name.
3170        my $genomeFileName = LoadFileName($dataDir, "Genome");
3171        # Extract the genome IDs from the files.
3172        my @retVal = map { $_ =~ /^(\S+)/; $1 } Tracer::GetFile($genomeFileName);
3173        # Return the result.
3174        return @retVal;
3175    }
3176    
3177    =head3 LoadFileName
3178    
3179    C<< my $fileName = Sprout::LoadFileName($dataDir, $tableName); >>
3180    
3181    Return the name of the load file for the specified table in the specified data
3182    directory.
3183    
3184    =over 4
3185    
3186    =item dataDir
3187    
3188    Directory containing the Sprout load files.
3189    
3190    =item tableName
3191    
3192    Name of the table whose load file is desired.
3193    
3194    =item RETURN
3195    
3196    Returns the name of the file containing the load data for the specified table, or
3197    C<undef> if no load file is present.
3198    
3199    =back
3200    
3201    =cut
3202    #: Return Type $;
3203    sub LoadFileName {
3204        # Get the parameters.
3205        my ($dataDir, $tableName) = @_;
3206        # Declare the return variable.
3207        my $retVal;
3208        # Check for the various file names.
3209        if (-e "$dataDir/$tableName") {
3210            $retVal = "$dataDir/$tableName";
3211        } elsif (-e "$dataDir/$tableName.dtx") {
3212            $retVal = "$dataDir/$tableName.dtx";
3213        }
3214        # Return the result.
3215        return $retVal;
3216    }
3217    
3218  =head2 Internal Utility Methods  =head2 Internal Utility Methods
3219    
3220  =head3 ParseAssignment  =head3 ParseAssignment
# Line 2903  Line 3254 
3254      # Declare the return value.      # Declare the return value.
3255      my @retVal = ();      my @retVal = ();
3256      # Check to see if this is a functional assignment.      # Check to see if this is a functional assignment.
3257      my ($user, $type, $function) = split(/\n/, $text);      my ($type, $function) = split(/\n/, $text);
3258      if ($type =~ m/^set ([^ ]+) function to$/i) {      if ($type =~ m/^set ([^ ]+) function to$/i) {
3259          # Here it is, so we return the user name (which is in $1), the functional role text,          # Here it is, so we return the user name (which is in $1), the functional role text,
3260          # and the assigning user.          # and the assigning user.
3261          @retVal = ($1, $function, $user);          @retVal = ($1, $function);
3262      }      }
3263      # Return the result list.      # Return the result list.
3264      return @retVal;      return @retVal;
# Line 2935  Line 3286 
3286    
3287  sub FriendlyTimestamp {  sub FriendlyTimestamp {
3288      my ($timeValue) = @_;      my ($timeValue) = @_;
3289      my $retVal = strftime("%a %b %e %H:%M:%S %Y", localtime($timeValue));      my $retVal = localtime($timeValue);
3290      return $retVal;      return $retVal;
3291  }  }
3292    
# Line 2996  Line 3347 
3347      $self->Insert('HasProperty', { 'from-link' => $featureID, 'to-link' => $propID, evidence => $url });      $self->Insert('HasProperty', { 'from-link' => $featureID, 'to-link' => $propID, evidence => $url });
3348  }  }
3349    
3350    
3351    
3352  1;  1;

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